Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea.
BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
PLoS Negl Trop Dis. 2022 Sep 12;16(9):e0010763. doi: 10.1371/journal.pntd.0010763. eCollection 2022 Sep.
Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK).
A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes.
CONCLUSION/SIGNIFICANCE: Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.
全基因组测序在旨在提高对新兴病毒传播理解的基因组流行病学中起着关键作用。大别山病毒引起严重发热伴血小板减少综合征（SFTS），是一种人畜共患的蜱传病毒，对公共卫生构成重大威胁。我们旨在评估一种新型基于扩增子的纳米孔测序工具，以获得大别山病毒（也称为 SFTS 病毒 [SFTSV]）的全基因组序列，并调查韩国（ROK）野生蜱中的分子流行情况。
2019 年和 2020 年，在韩国京畿道和江原道共采集了 6593 只蜱。定量聚合酶链反应显示，在三只长角血蜱中有 SFTSV RNA 的存在。从坡州和城川捕获的长角血蜱中分离出两种 SFTSV 株。基于多重聚合酶链反应的纳米孔测序在一个小时的运行时间内提供了 SFTSV 的几乎全长三分体基因组序列。进行了系统发育和重配分析，以推断 SFTSV 之间的进化关系。系统发育分析将来自坡州的 SFTSV Hl19-31-4 和 Hl19-31-13 与所有节段的 B-1 亚基因型聚为一组。发现 SFTSV Hl20-8 的基因组组织与 B-1（L 节段）和 B-2（M 和 S 节段）亚基因型兼容，表明亚基因型之间存在自然重配。
结论/意义：基于扩增子的下一代测序是一种使用纳米孔平台对 SFTSV 进行全基因组测序的强大工具。SFTSV 的分子流行和地理分布增强了高分辨率的系统发育图谱，为流行地区新兴 SFTS 的精细预防提供了依据。我们的研究结果为基于基因组的 SFTSV 诊断中的快速全基因组测序和遗传多样性提供了重要见解。
